So I checked out 0.40 and the first time a page comes up, the tabs and titles don't show up for borderlayout on anything but the center. The pin button still shows, and so if I contract them and then expand them, the tabs and titles show up.
Example:

I can confirm this using a more reasonable set of includes (e.g. just yui-ext.js and yui-ext.css).
Another issue related to this is resizing regions via border dragging. They're not resizable and the resize handle doesn't appear til after the region is collapsed/expanded.
It's an issue without or without using a theme.